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Showing :
gene set testing
•
reset
7
votes
13
replies
2.3k
views
Test whether expression levels of two gene sets are significantly different
R
DESeq2
gene set testing
gene expression
7.5 years ago
Jon Bråte
▴ 250
4
votes
11
replies
2.0k
views
Dealing with duplicated genes in camera gene set testing
limma
camera
gene set testing
ensembl
updated 4.4 years ago by
Robert Castelo
★ 3.3k • written 4.4 years ago by
Jeremy Beales
▴ 10
6
votes
10
replies
1.8k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing
roast
mroast
differential gene expression
bioconductor
9.0 years ago
svlachavas
▴ 830
4
votes
6
replies
2.0k
views
Gene set Testing with Limma for Agilent IDs probes?
limma
agilent microarrays
gene set testing
annotation
7.3 years ago
Bouzid.a
▴ 20
7
votes
6
replies
3.2k
views
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
limma
mroast
barcodeplot
KEGG
gene set testing
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
svlachavas
▴ 830
1
vote
5
replies
2.1k
views
Confused by results from CAMERA gene set testing
limma
camera
gene set testing
8.1 years ago
claire.n.levy
▴ 10
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA
gene set testing
vooma
limma voom
gsea
updated 13 days ago by
Chris
▴ 10 • written 7.4 years ago by
Pekka Kohonen
▴ 190
3
votes
4
replies
1.6k
views
Competitive gene set testing between two sets of genes
gene set testing
camera
edger
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
le2336
▴ 20
1
vote
4
replies
1.3k
views
Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
limma
roast
statistics
source code
gene set testing
5.8 years ago • updated 5.7 years ago
Andrea Carenzo
• 0
2
votes
3
replies
1.4k
views
Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
limma
agilent microarrays
mroast
fry gene tests
gene set testing
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
svlachavas
▴ 830
7
votes
2
replies
1.4k
views
Pre-ranked camera gene set testing with edgeR results
limma
camera
cameraPR
edgeR
gene set testing
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
jamie.gearing
▴ 60
0
votes
1
reply
1.3k
views
GAGE function and the same.dir option
gage
gene set testing
updated 6.0 years ago by
Luo Weijun
★ 1.6k • written 6.0 years ago by
Aurora
▴ 20
0
votes
0
replies
637
views
Interpretation of mroast p-value results for gene set testing of specific molecular signatures using microarray data
mroast
camera
gene set testing
3.6 years ago
svlachavas
▴ 830
1
vote
0
replies
1.3k
views
Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
gsea
ncrna
coexpression
gene set analysis
gene set testing
8.1 years ago
m.fletcher
▴ 20
14 results • Page
1 of 1
Recent ...
Replies
Comment: Slightly different count plots from R and spreadsheet
by
ATpoint
★ 4.1k
I don't think it is the purpose of the support site to debug Excel behaviour. The issue might be how it combines replicates into a single v…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
Karosham.Reddy
• 0
Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?
Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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